def boolean_gating(gate_params):
points = gate_params['points']
points2 = gate_params['1']
boolean_op = gate_params['0']
reverse_gate = '0'
if 'reverse' in gate_params:
if (gate_params['reverse']):
reverse_gate = '1'
## Generate unique datastore path, ensuring uniqueness.
while True:
new_name = str(uuid1())
new_path = ds.generate_path(DATA_BUCKET, None, new_name)
if not ds.check_exists(new_path, None):
break
if (gate_params['tool'] == "boolean_gating"):
if (len(points)%2 == 0) and (len(points2)%2 == 0):
if (reverse_gate == '1'):
if (boolean_op == 'or'):
boolean_op = 'and'
elif (boolean_op == 'and'):
boolean_op = 'or'
else:
return generate_gating_feedback("fail", "The boolean operator must be either 'and' or 'or'")
gate1_points = " ".join(str(p) for p in points)
gate2_points = " ".join(str(p) for p in points2)
queue.gate_boolean(gate_params['filename'], new_name, boolean_op, 'poly', gate1_points, reverse_gate, 'poly', gate2_points, reverse_gate, gate_params['axes']['x'], gate_params['axes']['y'], gate_params['axes']['x'], gate_params['axes']['y']);
return generate_gating_feedback("success", "the boolean gating was performed correctly", new_name, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect, wrong number of arguments")
def file_complete(self, file_size):
self.file_handle.close()
self.upload.size = file_size
## Start analysis.
queue.visualise(self.name)
## Load balance instances in the background.
background.run(instances.balance, 0)
return self.upload
def balance(): ## Calculate ratio of tasks to instances and acceptable limits. (ratio, instance_count, task_count) = stats() lower_ratio_limit = CE_SCALING * (1 - CE_SLACK) upper_ratio_limit = CE_SCALING * (1 + CE_SLACK) ## If ratio is outside acceptable limits, kill or start instances. if (ratio < lower_ratio_limit and instance_count > MIN_INSTANCES) or (instance_count > MAX_INSTANCES): queue.kill() elif (ratio > upper_ratio_limit and instance_count < MAX_INSTANCES) or (instance_count < MIN_INSTANCES): start()
def change_axes(tool_params):
## Generate unique datastore path, ensuring uniqueness.
while True:
new_name = str(uuid1())
new_path = ds.generate_path(DATA_BUCKET, None, new_name)
if not ds.check_exists(new_path, None):
break
if tool_params['newAxes']['x'] == tool_params['newAxes']['y']:
return generate_gating_feedback("fail", "Please choose two different axes")
# todo: check if the axes exist.
queue.change_axis(tool_params['filename'], tool_params['newAxes']['x'], tool_params['newAxes']['y'], new_name)
return generate_gating_feedback("success","the axis change was performed", new_name, tool_params['filename'], tool_params['newAxes']['x'], tool_params['newAxes']['y'])
def multiple_gating(gate_params):
points = gate_params['points']
while True:
new_name = str(uuid1())
new_path = ds.generate_path(DATA_BUCKET, None, new_name)
if not ds.check_exists(new_path, None):
break
if (gate_params['tool'] == 'kmeans_gating') :
if len(points) == 1 :
clusters = new_name
number_gates = points[0]
new_names = [new_name]
for i in range(0, number_gates-1):
while True:
next_new_name = str(uuid1())
path = ds.generate_path(DATA_BUCKET, None, next_new_name)
if not ds.check_exists(path, None):
new_names.append(next_new_name)
clusters = next_new_name + " " + clusters
break
queue.gate_kmeans(gate_params['filename'], clusters, str(number_gates), gate_params['axes']['x'], gate_params['axes']['y']);
return generate_gating_feedback("success", "the kmeans gate was performed correctly", new_names, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect, wrong number of arguments")
elif (gate_params['tool'] == 'quadrant_gating') :
if len(points) == 2 :
other_new_names = []
for i in range(0, 3):
while True:
next_new_name = str(uuid1())
path = ds.generate_path(DATA_BUCKET, None, next_new_name)
if not ds.check_exists(path, None):
other_new_names.append(next_new_name)
break
x_coord = str(points[0])
y_coord = str(points[1])
queue.gate_quadrant(gate_params['filename'], x_coord, y_coord, new_name, other_new_names[0], other_new_names[1], other_new_names[2], gate_params['axes']['x'], gate_params['axes']['y']);
new_paths = [new_name] + other_new_names
new_paths.reverse() #Make sure the user polls for the last graph to be created
return generate_gating_feedback("success", "the quadrant gate was performed correctly", new_paths, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect, wrong number of arguments")
def stats():
instance_count = count()
task_count = queue.task_count()
if instance_count == 0:
if task_count == 0:
ratio = 1
else:
ratio = float('inf')
else:
ratio = task_count / instance_count
return (ratio, instance_count, task_count)
'gate_cir' : shape_gating,
'gate_poly' : shape_gating,
'gate_bool' : shape_gating,
'change_axis' : axis_change,
'dot_plot' : change_plot,
'contour_plot' : change_plot,
'gate_quad' : quadrant_gate,
'gate_norm' : data_gate,
'gate_kmeans' : data_gate
}
# Check task queue until 'kill' command is received.
alive = True
while alive:
# Lease a command.
try:
task = Queue.lease('jobs', 30)
except Exception, e:
print e
# If there are tasks in queue extract id and commands, else restart loop and check queue again.
if task is not None:
task_id = task[0]
commands = task[1]
else:
time.sleep(0.9)
continue
functionToCall = AVAILABLE_TASKS[commands[0]]
alive = functionToCall(commands)
# Delete any processed tasks from queue.
if task_id is not None:
Queue.delete('jobs', task_id)
def simple_gating(gate_params):
points = gate_params['points']
reverse_gate = '0'
if 'reverse' in gate_params:
if (gate_params['reverse']):
reverse_gate = '1'
## Generate unique datastore path, ensuring uniqueness.
while True:
new_name = str(uuid1())
new_path = ds.generate_path(DATA_BUCKET, None, new_name)
if not ds.check_exists(new_path, None):
break
if (gate_params['tool'] == "rectangular_gating") :
if len(points) == 4 :
#Reoder the point to take the topLeft and bottomRight points of the square
if points[0] > points[2]:
tempcoor = points[0]
points[0] = points[2]
points[2] = tempcoor
if points[1] > points[3]:
tempcoor = points[1]
points[1] = points[3]
points[3] = tempcoor
gating_request = " ".join(str(p) for p in points)
queue.gate_rectangle(gate_params['filename'], gating_request, new_name, reverse_gate, gate_params['axes']['x'], gate_params['axes']['y']);
return generate_gating_feedback("success", "the rectangular gating was performed correctly", new_name, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect " + params + " length:" + str(len(points)) + " is not equal to 4")
elif (gate_params['tool'] == "polygon_gating") :
if len(points)%2 == 0 :
gating_request = " ".join(str(p) for p in points)
queue.gate_polygon(gate_params['filename'], gating_request, new_name, reverse_gate, gate_params['axes']['x'], gate_params['axes']['y']);
return generate_gating_feedback("success", "the polygonal gating was performed correctly", new_name, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect " + params + " #pointCoordinates:" + str(len(points))-1 + " is not pair")
elif (gate_params['tool'] == "oval_gating") :
if len(points) == 6 :
gating_request = " ".join(str(p) for p in points)
queue.gate_circle(gate_params['filename'], gating_request, new_name, reverse_gate, gate_params['axes']['x'], gate_params['axes']['y']);
return generate_gating_feedback("success", "the oval gating was performed correctly", new_name, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect " + params + " #pointCoordinates:" + str(len(points)) + " is not even")
elif (gate_params['tool'] == 'normal_gating') :
if len(points) == 1 :
gating_request = str(points[0])
queue.gate_normal(gate_params['filename'], new_name, reverse_gate, gate_params['axes']['x'], gate_params['axes']['y'], gating_request);
return generate_gating_feedback("success", "the normal gating was performed correctly", new_name, gate_params['filename'], gate_params['axes']['x'], gate_params['axes']['y'])
else:
return generate_gating_feedback("fail", "notcorrect, wrong number of arguments")
else :
return generate_gating_feedback("fail", "The gate " + gate_params['tool'] + " is not known")
